At the Wow-O Toy Factory, the Mystery Inc. group found the Luna Ghost, who has been haunting the factory. Once the Luna Ghost was accidentally falling into a bunch of dolls, Pamela Anderson arrived to give coverage of the Luna Ghost's unmasking. The Luna Ghost happened to be Old Man Smithers, the creepy janitor of the factory who was turned down a date by Pamela Anderson. While the mystery was solved, several disagreements between the group made go their own ways, with the exception of Shaggy and Scooby.
After two years, the former members of Mystery Inc. were given invitations to Spooky Island, an amusement park at a haunted island. Shaggy and Scooby declined at first but decided to join because of the "all you can eat" deal. Velma worked at NASA, Fred became a celebrity author and Daphne trained in martial arts as a black belt to prevent herself from being the Damsel in Distress.
On the way to Spooky Island, Shaggy met a college girl named Mary Jane who has a craving for Scooby Snacks. As they arrived at Spooky Island, they met the founder of the amusement park, Emile Mondavarious. He brought the Mystery Inc. crew together to solve a mystery because the people in the island have been brainwashed. Ngoo Tauna told the visitors that Emile Mondavarious founded the theme park ten years ago after he witnessed slim purple monsters that inhabit the island. Daphne paid a visit to the Voodoo Maestro who warned her to never enter the Spooky Island castle. She took that as an act of reverse psychology and the entire gang went inside. Inside the castle, it is actually a ride that has yet to be finished. The crew found a room where a video shows people being brainwashed with slang and threats for their speech. At a hidden room, Daphne found a mysterious device known as the Daemon Ritus.
At the hotel in Spooky Island, the crew figured out the three suspects of the case: the Voodoo Maestro, Ngoo Tauna and Emile Mondavarious. All of a sudden, the purple monsters of Spooky Island wrecked the hotel and took several of the guests, including Daphne, Velma and Fred. Scooby, Shaggy and Mary Jane leave the hotel in the nick of time.
The next day, the hotel was mysteriously repaired. Shaggy encountered Fred at a nearby pool with the latter saying terms such as "biyatch". Scooby, Shaggy and Mary Jane drove to where Ngoo Tauna gave his speech the night before. Scooby and Shaggy jumped into the pit and found a pool of protoplasm. Shaggy found the protoplasms of Daphne, Velma and Fred and made them fly back to their possessed bodies. As Velma is restored, the purple monster that took control of her emerged and was destroyed by the sunlight. Velma went into Daphne's room and found out that Daphne has Fred's protoplasm. As with before, she used the sunlight to kill the demon from Daphne's body. Daphne's protoplasm entered into Fred's body. As the gang regrouped, they learned that the Daemon Ritus can make the user switch bodies at a quick rate. As their bodies are in the right position, they devised a plan to prevent Emile Mondavarious from beginning the Darkopalypse.
Scooby was taken by Emile Mondavarious as a sacrifice. This made Velma realize that in order for Emile Mondavarious to start the Darkopalypse, he needs a pure soul. "I didn't say human." As the Darkopalypse begins, Shaggy disguised himself as a Spooky Island guard to comfort Scooby-Doo. Daphne was taken by Ngoo Tauna's henchman, Zarkos. Before Emile starts to absorb Scooby's protoplasm with the Daemon Ritus, he was whacked by the operator. Fred and Velma unmasked him, revealing to be a robot operated by none other than Scooby's nephew, Scrappy-Doo, who was kicked out of Mystery Inc. before the Luna Ghost case for being an ego-driven narcissist. With all of the absorbed protoplasms, Scrappy became Scrappy Rex.
As Shaggy, Scooby and Mary Jane try to hide from Scrappy Rex, Daphne defeated Zarkos and made him land on the pool of protoplasm, restoring the bodies of all the visitors. And with the Disco Skull, it's light was able to kill all the demons. Because of this, Scrappy Rex reverted back to Scrappy-Doo. The real Emile Mondavarious was freed and thanked the crew for defeating his captor.
Scrappy-Doo, Ngoo Tauna and Zarkos were imprisioned and the Mystery Inc. crew is up to stop the Mud Bog Ghoul from terrorizing England. However, Shaggy and Scooby didn't forget about the all-you-can-eat deal that was promised. Hilarity ensues.